Magnesium in PDB 6sge: Crystal Structure of Human Rhob-Gtp in Complex with Nanobody B6
Protein crystallography data
The structure of Crystal Structure of Human Rhob-Gtp in Complex with Nanobody B6, PDB code: 6sge
was solved by
S.Soulie,
R.Gence,
S.Cabantous,
I.Lajoie-Mazenc,
G.Favre,
J.D.Pedelacq,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
47.18 /
1.50
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
66.840,
70.227,
71.212,
90.00,
107.68,
90.00
|
|
R / Rfree (%)
|
16.1 /
18.8
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Human Rhob-Gtp in Complex with Nanobody B6
(pdb code 6sge). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Crystal Structure of Human Rhob-Gtp in Complex with Nanobody B6, PDB code: 6sge:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6sge
Go back to
Magnesium Binding Sites List in 6sge
Magnesium binding site 1 out
of 4 in the Crystal Structure of Human Rhob-Gtp in Complex with Nanobody B6
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of Human Rhob-Gtp in Complex with Nanobody B6 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg202
b:15.0
occ:1.00
|
H1
|
A:GTP201
|
1.7
|
17.8
|
1.0
|
|
O1G
|
A:GTP201
|
2.0
|
14.8
|
1.0
|
|
O2B
|
A:GTP201
|
2.0
|
14.0
|
1.0
|
|
OG1
|
A:THR19
|
2.1
|
18.3
|
1.0
|
|
O
|
A:HOH362
|
2.1
|
15.9
|
1.0
|
|
OG1
|
A:THR37
|
2.1
|
18.9
|
1.0
|
|
O
|
A:HOH316
|
2.2
|
15.3
|
1.0
|
|
H
|
A:THR37
|
3.0
|
19.2
|
1.0
|
|
HB
|
A:THR19
|
3.0
|
19.4
|
1.0
|
|
HB
|
A:THR37
|
3.1
|
21.3
|
1.0
|
|
CB
|
A:THR19
|
3.1
|
16.2
|
1.0
|
|
CB
|
A:THR37
|
3.1
|
17.8
|
1.0
|
|
PG
|
A:GTP201
|
3.1
|
16.0
|
1.0
|
|
PB
|
A:GTP201
|
3.2
|
15.5
|
1.0
|
|
H
|
A:THR19
|
3.2
|
18.0
|
1.0
|
|
O3B
|
A:GTP201
|
3.4
|
15.3
|
1.0
|
|
N
|
A:THR37
|
3.7
|
16.0
|
1.0
|
|
N
|
A:THR19
|
3.9
|
15.0
|
1.0
|
|
HB2
|
A:LYS18
|
4.0
|
16.3
|
1.0
|
|
CA
|
A:THR37
|
4.0
|
17.0
|
1.0
|
|
O2G
|
A:GTP201
|
4.0
|
15.7
|
1.0
|
|
HG21
|
A:THR19
|
4.0
|
21.8
|
1.0
|
|
CA
|
A:THR19
|
4.1
|
16.0
|
1.0
|
|
HG21
|
A:THR37
|
4.1
|
19.8
|
1.0
|
|
O2A
|
A:GTP201
|
4.1
|
16.7
|
1.0
|
|
OD2
|
A:ASP59
|
4.1
|
18.3
|
1.0
|
|
OD1
|
A:ASP59
|
4.2
|
17.4
|
1.0
|
|
CG2
|
A:THR37
|
4.2
|
16.5
|
1.0
|
|
CG2
|
A:THR19
|
4.2
|
18.2
|
1.0
|
|
O3A
|
A:GTP201
|
4.2
|
15.0
|
1.0
|
|
O
|
A:HOH319
|
4.2
|
19.7
|
1.0
|
|
HE2
|
A:LYS18
|
4.2
|
18.0
|
1.0
|
|
O1B
|
A:GTP201
|
4.3
|
14.6
|
1.0
|
|
HA
|
A:PRO36
|
4.3
|
20.6
|
1.0
|
|
HE1
|
A:TYR34
|
4.4
|
20.6
|
1.0
|
|
HA
|
A:THR19
|
4.4
|
19.2
|
1.0
|
|
HZ2
|
A:LYS18
|
4.4
|
18.0
|
1.0
|
|
HA
|
A:THR37
|
4.4
|
20.4
|
1.0
|
|
CG
|
A:ASP59
|
4.5
|
16.7
|
1.0
|
|
O
|
A:THR60
|
4.5
|
15.3
|
1.0
|
|
PA
|
A:GTP201
|
4.5
|
15.9
|
1.0
|
|
O3G
|
A:GTP201
|
4.5
|
25.8
|
1.0
|
|
O
|
A:VAL35
|
4.5
|
18.9
|
1.0
|
|
HG23
|
A:THR37
|
4.6
|
19.8
|
1.0
|
|
HOG2
|
A:GTP201
|
4.6
|
18.8
|
1.0
|
|
O1A
|
A:GTP201
|
4.7
|
16.0
|
1.0
|
|
C
|
A:PRO36
|
4.7
|
17.9
|
1.0
|
|
HG23
|
A:THR19
|
4.8
|
21.8
|
1.0
|
|
HG22
|
A:THR19
|
4.8
|
21.8
|
1.0
|
|
HA
|
A:ALA61
|
4.9
|
19.9
|
1.0
|
|
CB
|
A:LYS18
|
4.9
|
13.6
|
1.0
|
|
HG22
|
A:THR37
|
4.9
|
19.8
|
1.0
|
|
CA
|
A:PRO36
|
5.0
|
17.2
|
1.0
|
|
C
|
A:LYS18
|
5.0
|
16.6
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6sge
Go back to
Magnesium Binding Sites List in 6sge
Magnesium binding site 2 out
of 4 in the Crystal Structure of Human Rhob-Gtp in Complex with Nanobody B6
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of Human Rhob-Gtp in Complex with Nanobody B6 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg203
b:24.3
occ:1.00
|
HH
|
D:TYR60
|
1.9
|
22.9
|
1.0
|
|
O
|
A:ASP59
|
2.7
|
16.9
|
1.0
|
|
HB3
|
A:TRP58
|
2.7
|
20.7
|
1.0
|
|
OG
|
A:SER73
|
2.7
|
18.5
|
1.0
|
|
OH
|
D:TYR60
|
2.7
|
19.1
|
1.0
|
|
HE2
|
D:TYR60
|
2.8
|
22.4
|
1.0
|
|
HE3
|
A:TRP58
|
2.8
|
21.8
|
1.0
|
|
H
|
A:GLU40
|
3.1
|
21.8
|
1.0
|
|
HB2
|
A:PHE39
|
3.1
|
21.4
|
1.0
|
|
O
|
A:GLU40
|
3.1
|
17.8
|
1.0
|
|
H
|
A:ASP59
|
3.1
|
19.2
|
1.0
|
|
HG
|
A:SER73
|
3.2
|
22.2
|
1.0
|
|
N
|
A:ASP59
|
3.4
|
16.0
|
1.0
|
|
CE2
|
D:TYR60
|
3.4
|
18.7
|
1.0
|
|
HA
|
A:TRP58
|
3.5
|
19.1
|
1.0
|
|
CZ
|
D:TYR60
|
3.5
|
19.9
|
1.0
|
|
C
|
A:ASP59
|
3.5
|
15.4
|
1.0
|
|
CB
|
A:TRP58
|
3.5
|
17.3
|
1.0
|
|
CE3
|
A:TRP58
|
3.6
|
18.2
|
1.0
|
|
HB3
|
A:SER73
|
3.6
|
22.3
|
1.0
|
|
C
|
A:TRP58
|
3.7
|
16.7
|
1.0
|
|
N
|
A:GLU40
|
3.7
|
18.2
|
1.0
|
|
HG22
|
A:THR60
|
3.7
|
21.0
|
1.0
|
|
CA
|
A:TRP58
|
3.8
|
15.9
|
1.0
|
|
CB
|
A:SER73
|
3.8
|
18.6
|
1.0
|
|
HB3
|
A:ASN41
|
3.8
|
24.5
|
1.0
|
|
C
|
A:GLU40
|
3.9
|
19.4
|
1.0
|
|
CB
|
A:PHE39
|
4.0
|
17.8
|
1.0
|
|
CA
|
A:ASP59
|
4.1
|
15.2
|
1.0
|
|
HA
|
A:PHE39
|
4.1
|
21.0
|
1.0
|
|
HG23
|
A:THR60
|
4.2
|
21.0
|
1.0
|
|
CD2
|
A:TRP58
|
4.2
|
19.4
|
1.0
|
|
HB2
|
A:TRP58
|
4.2
|
20.7
|
1.0
|
|
CG
|
A:TRP58
|
4.2
|
17.8
|
1.0
|
|
O
|
A:HOH313
|
4.3
|
19.4
|
1.0
|
|
HA
|
A:THR60
|
4.3
|
17.9
|
1.0
|
|
HB3
|
A:PHE39
|
4.3
|
21.4
|
1.0
|
|
CA
|
A:GLU40
|
4.4
|
18.9
|
1.0
|
|
O
|
A:TRP58
|
4.4
|
16.4
|
1.0
|
|
HB2
|
A:SER73
|
4.4
|
22.3
|
1.0
|
|
CG2
|
A:THR60
|
4.4
|
17.5
|
1.0
|
|
CA
|
A:PHE39
|
4.4
|
17.5
|
1.0
|
|
HA
|
A:SER73
|
4.5
|
22.6
|
1.0
|
|
C
|
A:PHE39
|
4.5
|
18.5
|
1.0
|
|
HD1
|
A:PHE39
|
4.5
|
26.2
|
1.0
|
|
N
|
A:THR60
|
4.5
|
15.3
|
1.0
|
|
CZ3
|
A:TRP58
|
4.6
|
20.3
|
1.0
|
|
HZ3
|
A:TRP58
|
4.6
|
24.4
|
1.0
|
|
HA
|
A:GLU40
|
4.6
|
22.6
|
1.0
|
|
CD2
|
D:TYR60
|
4.7
|
19.4
|
1.0
|
|
HD22
|
A:ASN41
|
4.7
|
26.2
|
1.0
|
|
HB3
|
A:ASP59
|
4.7
|
19.2
|
1.0
|
|
CB
|
A:ASN41
|
4.7
|
20.4
|
1.0
|
|
CA
|
A:SER73
|
4.7
|
18.8
|
1.0
|
|
N
|
A:ASN41
|
4.8
|
18.9
|
1.0
|
|
HA
|
A:ASP59
|
4.8
|
18.2
|
1.0
|
|
CE1
|
D:TYR60
|
4.8
|
20.4
|
1.0
|
|
HA
|
A:ASN41
|
4.8
|
23.3
|
1.0
|
|
CA
|
A:THR60
|
4.9
|
14.9
|
1.0
|
|
CG
|
A:PHE39
|
4.9
|
19.4
|
1.0
|
|
CB
|
A:ASP59
|
5.0
|
16.0
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6sge
Go back to
Magnesium Binding Sites List in 6sge
Magnesium binding site 3 out
of 4 in the Crystal Structure of Human Rhob-Gtp in Complex with Nanobody B6
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of Human Rhob-Gtp in Complex with Nanobody B6 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg202
b:14.9
occ:1.00
|
H1
|
C:GTP201
|
1.9
|
18.4
|
1.0
|
|
O1G
|
C:GTP201
|
2.0
|
15.3
|
1.0
|
|
O2B
|
C:GTP201
|
2.0
|
13.9
|
1.0
|
|
OG1
|
C:THR19
|
2.0
|
18.6
|
1.0
|
|
OG1
|
C:THR37
|
2.1
|
18.4
|
1.0
|
|
O
|
C:HOH315
|
2.1
|
15.3
|
1.0
|
|
O
|
C:HOH345
|
2.1
|
16.7
|
1.0
|
|
HB
|
C:THR19
|
3.0
|
18.6
|
1.0
|
|
HB
|
C:THR37
|
3.0
|
20.0
|
1.0
|
|
CB
|
C:THR19
|
3.1
|
15.5
|
1.0
|
|
CB
|
C:THR37
|
3.1
|
16.6
|
1.0
|
|
H
|
C:THR37
|
3.1
|
19.2
|
1.0
|
|
PG
|
C:GTP201
|
3.2
|
15.7
|
1.0
|
|
PB
|
C:GTP201
|
3.2
|
14.6
|
1.0
|
|
H
|
C:THR19
|
3.3
|
18.0
|
1.0
|
|
O3B
|
C:GTP201
|
3.4
|
15.1
|
1.0
|
|
N
|
C:THR37
|
3.7
|
16.0
|
1.0
|
|
N
|
C:THR19
|
3.9
|
15.0
|
1.0
|
|
HB2
|
C:LYS18
|
4.0
|
16.2
|
1.0
|
|
CA
|
C:THR37
|
4.0
|
14.8
|
1.0
|
|
O2G
|
C:GTP201
|
4.0
|
16.3
|
1.0
|
|
HG21
|
C:THR19
|
4.0
|
20.9
|
1.0
|
|
CA
|
C:THR19
|
4.0
|
13.8
|
1.0
|
|
OD2
|
C:ASP59
|
4.1
|
19.9
|
1.0
|
|
O2A
|
C:GTP201
|
4.1
|
16.7
|
1.0
|
|
HG21
|
C:THR37
|
4.1
|
20.0
|
1.0
|
|
OD1
|
C:ASP59
|
4.2
|
16.8
|
1.0
|
|
CG2
|
C:THR19
|
4.2
|
17.4
|
1.0
|
|
CG2
|
C:THR37
|
4.2
|
16.6
|
1.0
|
|
HE2
|
C:LYS18
|
4.2
|
18.2
|
1.0
|
|
O
|
C:HOH323
|
4.2
|
19.7
|
1.0
|
|
O3A
|
C:GTP201
|
4.2
|
15.5
|
1.0
|
|
HA
|
C:PRO36
|
4.3
|
20.5
|
1.0
|
|
O1B
|
C:GTP201
|
4.3
|
14.4
|
1.0
|
|
HA
|
C:THR19
|
4.3
|
16.6
|
1.0
|
|
HA
|
C:THR37
|
4.4
|
17.7
|
1.0
|
|
CG
|
C:ASP59
|
4.4
|
17.3
|
1.0
|
|
HZ3
|
C:LYS18
|
4.4
|
17.0
|
1.0
|
|
HE1
|
C:TYR34
|
4.5
|
21.9
|
1.0
|
|
O
|
C:THR60
|
4.5
|
14.5
|
1.0
|
|
PA
|
C:GTP201
|
4.5
|
16.6
|
1.0
|
|
O3G
|
C:GTP201
|
4.6
|
27.6
|
1.0
|
|
O
|
C:VAL35
|
4.6
|
19.1
|
1.0
|
|
HG23
|
C:THR37
|
4.6
|
20.0
|
1.0
|
|
HOG2
|
C:GTP201
|
4.7
|
19.6
|
1.0
|
|
HG23
|
C:THR19
|
4.7
|
20.9
|
1.0
|
|
C
|
C:PRO36
|
4.7
|
17.2
|
1.0
|
|
O1A
|
C:GTP201
|
4.8
|
16.2
|
1.0
|
|
HA
|
C:ALA61
|
4.8
|
19.5
|
1.0
|
|
HG22
|
C:THR19
|
4.9
|
20.9
|
1.0
|
|
CB
|
C:LYS18
|
4.9
|
13.5
|
1.0
|
|
HG22
|
C:THR37
|
5.0
|
20.0
|
1.0
|
|
C
|
C:LYS18
|
5.0
|
15.8
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6sge
Go back to
Magnesium Binding Sites List in 6sge
Magnesium binding site 4 out
of 4 in the Crystal Structure of Human Rhob-Gtp in Complex with Nanobody B6
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of Human Rhob-Gtp in Complex with Nanobody B6 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg203
b:23.2
occ:1.00
|
H
|
C:ALA61
|
2.2
|
19.1
|
1.0
|
|
O
|
C:VAL38
|
2.7
|
16.8
|
1.0
|
|
O
|
C:HOH372
|
2.7
|
16.7
|
1.0
|
|
HB3
|
C:PHE39
|
2.8
|
20.4
|
1.0
|
|
HA
|
C:THR60
|
2.8
|
17.1
|
1.0
|
|
O
|
C:HOH326
|
2.8
|
17.8
|
1.0
|
|
N
|
C:ALA61
|
3.0
|
15.9
|
1.0
|
|
HA
|
C:ARG70
|
3.1
|
20.0
|
1.0
|
|
HB
|
C:THR60
|
3.2
|
18.4
|
1.0
|
|
HB3
|
C:ALA61
|
3.4
|
20.8
|
1.0
|
|
CA
|
C:THR60
|
3.5
|
14.2
|
1.0
|
|
HB2
|
C:LEU69
|
3.5
|
25.1
|
1.0
|
|
HG22
|
C:THR60
|
3.6
|
19.7
|
1.0
|
|
HB2
|
C:ALA61
|
3.7
|
20.8
|
1.0
|
|
CB
|
C:PHE39
|
3.7
|
17.0
|
1.0
|
|
CB
|
C:THR60
|
3.7
|
15.3
|
1.0
|
|
C
|
C:THR60
|
3.8
|
13.6
|
1.0
|
|
CB
|
C:ALA61
|
3.8
|
17.3
|
1.0
|
|
C
|
C:VAL38
|
3.9
|
16.5
|
1.0
|
|
HA
|
C:PHE39
|
3.9
|
19.1
|
1.0
|
|
HD2
|
C:PHE39
|
3.9
|
23.0
|
1.0
|
|
CA
|
C:ALA61
|
4.0
|
16.2
|
1.0
|
|
HB3
|
C:LEU69
|
4.0
|
25.1
|
1.0
|
|
N
|
C:ARG70
|
4.0
|
18.9
|
1.0
|
|
CA
|
C:ARG70
|
4.0
|
16.7
|
1.0
|
|
HG3
|
C:ARG70
|
4.1
|
19.7
|
1.0
|
|
HB2
|
C:PHE39
|
4.1
|
20.4
|
1.0
|
|
H
|
C:ARG70
|
4.2
|
22.7
|
1.0
|
|
CG2
|
C:THR60
|
4.2
|
16.4
|
1.0
|
|
C
|
C:LEU69
|
4.2
|
18.1
|
1.0
|
|
CB
|
C:LEU69
|
4.2
|
20.9
|
1.0
|
|
O
|
C:LEU69
|
4.2
|
18.7
|
1.0
|
|
CA
|
C:PHE39
|
4.3
|
15.9
|
1.0
|
|
HG
|
C:SER73
|
4.3
|
20.3
|
1.0
|
|
HB3
|
C:TYR66
|
4.4
|
30.2
|
1.0
|
|
O
|
C:ALA61
|
4.5
|
17.3
|
1.0
|
|
N
|
C:PHE39
|
4.5
|
16.3
|
1.0
|
|
O
|
C:ASP59
|
4.6
|
14.6
|
1.0
|
|
CD2
|
C:PHE39
|
4.6
|
19.2
|
1.0
|
|
HE
|
C:ARG70
|
4.6
|
19.8
|
1.0
|
|
HG21
|
C:THR60
|
4.6
|
19.7
|
1.0
|
|
HG22
|
C:THR37
|
4.6
|
20.0
|
1.0
|
|
CG
|
C:PHE39
|
4.7
|
18.4
|
1.0
|
|
HA
|
C:ALA61
|
4.7
|
19.5
|
1.0
|
|
HB2
|
C:ARG70
|
4.7
|
20.9
|
1.0
|
|
C
|
C:ALA61
|
4.7
|
16.9
|
1.0
|
|
HB1
|
C:ALA61
|
4.8
|
20.8
|
1.0
|
|
N
|
C:THR60
|
4.8
|
14.5
|
1.0
|
|
CB
|
C:ARG70
|
4.8
|
17.4
|
1.0
|
|
HD12
|
C:LEU69
|
4.8
|
32.2
|
1.0
|
|
OG
|
C:SER73
|
4.8
|
16.9
|
1.0
|
|
CG
|
C:ARG70
|
4.9
|
16.4
|
1.0
|
|
CA
|
C:LEU69
|
4.9
|
21.0
|
1.0
|
|
O
|
C:TYR66
|
4.9
|
22.6
|
1.0
|
|
HG23
|
C:THR60
|
4.9
|
19.7
|
1.0
|
|
HA
|
C:VAL38
|
4.9
|
20.4
|
1.0
|
|
O
|
C:THR60
|
5.0
|
14.5
|
1.0
|
|
OG1
|
C:THR60
|
5.0
|
16.5
|
1.0
|
|
Reference:
N.Bery,
L.Keller,
M.Soulie,
R.Gence,
A.L.Iscache,
J.Cherier,
S.Cabantous,
O.Sordet,
I.Lajoie-Mazenc,
J.D.Pedelacq,
G.Favre,
A.Olichon.
A Targeted Protein Degradation Cell-Based Screening For Nanobodies Selective Toward the Cellular Rhob Gtp-Bound Conformation. Cell Chem Biol V. 26 1544 2019.
ISSN: ESSN 2451-9456
PubMed: 31522999
DOI: 10.1016/J.CHEMBIOL.2019.08.009
Page generated: Tue Oct 1 17:56:33 2024
|
